Due to the stochastic nature of nucleic acid amplification, mutated species of nucleic acid are often difficult to detect. For example, when a wild-type sequence is present in a sample in vast excess relative to a mutant sequence, it is statistically unlikely that the mutant sequence will be amplified using primers that span the mutation (i.e., only the wild-type templates will be amplified). This problem is compounded in the situation in which there is a recombinant event between two genes, resulting in a subpopulation of recombinant, or chimeric, nucleic acids (i.e., containing a portion of a first wild-type nucleic acid and a portion of a second wild-type nucleic acid). Amplification of the chimeric nucleic acid is complicated not only by the stochastic effects described above but also by interference from the wild-type nucleic acid. Any primers intended to amplify only one of the two segments of the chimeric nucleic acid will necessarily also amplify the corresponding wild-type nucleic acid (e.g. the full length wild-type nucleic acid), resulting in the inability to determine which amplicons come from the chimera.